Contacts of the strand formed by residues 264 - 275 (chain F) in PDB entry 4U8T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 264 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199F ILE* 3.2 3.6 - - - +
200F TRP* 2.8 56.8 + + + +
201F SER* 4.2 0.7 - - - -
202F SER 4.6 0.2 - - - -
207F ASN* 3.7 20.0 - - - -
210F LEU* 3.6 31.4 - - + -
225F LEU* 4.1 5.4 - - + -
241F MSE 3.7 33.2 - - + -
243F SER* 3.5 12.3 - - - +
244F ASN 3.3 21.5 - - - +
245F LEU* 3.5 17.9 - - + -
249F LEU* 3.9 7.2 - - - -
263F ALA* 1.3 74.3 - - - +
265F LYS* 1.3 64.3 + - - +
266F VAL* 3.9 18.8 - - + -
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Residues in contact with LYS 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F GLY 3.5 7.9 - - - +
199F ILE* 4.2 6.7 - - + +
241F MSE 3.6 1.7 - - - -
242F SER* 2.7 43.0 + - - +
243F SER* 3.1 23.6 + - - +
246F ARG* 4.1 23.5 - - - +
249F LEU* 4.2 20.6 - - + -
264F PHE* 1.3 78.4 - - - +
266F VAL* 1.3 55.9 + - - +
267F ARG* 5.4 7.7 - - - +
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Residues in contact with VAL 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F SER* 4.0 3.4 - - - +
198F GLY* 2.8 42.0 + - - +
199F ILE 3.7 10.3 - - - +
200F TRP* 4.0 10.8 - - + -
225F LEU* 4.1 11.2 - - + -
227F PHE* 5.5 0.7 - - + -
239F ALA* 4.4 8.1 - - + -
240F GLU 3.1 15.5 - - - +
242F SER* 3.3 5.9 + - - -
264F PHE* 3.9 24.9 - - + -
265F LYS* 1.3 78.2 - - - +
267F ARG* 1.3 60.1 + - - +
268F TRP* 4.0 24.6 + - - +
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Residues in contact with ARG 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F LYS* 4.9 11.5 - - - +
239F ALA* 3.4 1.1 - - - -
240F GLU* 2.9 52.4 + - - +
242F SER* 3.7 30.4 + - - -
265F LYS* 5.4 7.9 - - - +
266F VAL* 1.3 72.4 + - - +
268F TRP* 1.3 70.2 + - - +
269F ILE* 3.5 7.0 + - + +
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Residues in contact with TRP 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F VAL* 3.6 25.4 - - + -
194F SER* 3.2 40.4 + - - -
195F PHE* 3.3 43.4 - + + +
198F GLY* 5.0 1.6 - - - -
227F PHE* 3.5 42.6 - + + -
237F GLY* 4.0 21.8 - - - -
238F VAL 3.7 15.0 - - - -
239F ALA* 3.8 9.9 - - + -
266F VAL* 3.9 15.4 + - + +
267F ARG* 1.3 77.5 - - - +
269F ILE* 1.3 59.6 + - - +
270F VAL 3.8 8.7 - - - -
271F VAL* 4.1 8.5 - - + -
323F PHE* 4.3 8.7 - + - -
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Residues in contact with ILE 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ILE* 4.2 13.2 - - - +
169F PRO* 3.5 27.7 - - + +
171F TRP 5.3 0.4 - - - +
172F ILE* 4.3 17.0 - - + -
224F TYR* 3.7 18.6 - - + -
238F VAL* 2.8 15.6 + - + +
240F GLU* 3.2 37.9 - - + +
267F ARG* 3.8 12.3 - - + +
268F TRP* 1.3 77.0 - - - +
270F VAL* 1.3 77.8 + - + +
271F VAL* 5.5 0.4 - - - -
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Residues in contact with VAL 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ILE 3.7 9.9 - - - +
168F ILE* 4.9 0.4 - - - -
169F PRO* 3.5 22.9 - - + -
172F ILE* 3.7 15.0 - - + -
237F GLY* 3.1 2.4 - - - -
238F VAL* 2.8 45.2 + - + +
268F TRP* 3.8 1.7 - - - -
269F ILE* 1.3 91.3 - - + +
271F VAL* 1.3 72.0 + - - +
272F ARG* 4.3 6.3 - - + -
313F PHE* 3.8 42.2 - - + +
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Residues in contact with VAL 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ALA* 3.3 6.4 - - - +
167F ILE* 2.9 45.4 + - + +
195F PHE* 4.0 31.2 - - + -
236F CYS 4.0 2.9 - - - -
268F TRP* 4.1 9.6 - - + -
269F ILE 5.5 0.2 - - - -
270F VAL* 1.3 78.9 - - - +
272F ARG* 1.3 63.1 + - - +
322F SER* 4.2 12.6 - - - -
323F PHE* 3.4 40.8 - - + -
324F LEU* 4.2 11.9 - - + -
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Residues in contact with ARG 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ALA* 4.7 1.3 - - + -
168F ILE* 4.0 18.2 - - + +
235F PHE 3.6 1.0 - - - +
236F CYS* 3.1 27.7 + - - -
237F GLY* 3.6 2.2 + - - -
270F VAL* 4.0 10.4 - - + -
271F VAL* 1.3 77.1 - - - +
273F ASP* 1.3 81.2 + - - +
274F VAL* 3.6 9.5 + - + +
312F LEU 3.6 11.0 + - - -
313F PHE* 3.6 24.3 + - + +
315F TYR* 2.9 54.2 - - - +
320F VAL* 4.2 25.8 - - + +
321F GLN 3.6 11.7 - - - +
322F SER* 4.2 2.7 - - - -
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Residues in contact with ASP 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F ARG* 3.0 46.5 + - - +
235F PHE 3.4 3.8 - - - -
236F CYS* 3.7 17.8 - - - +
272F ARG* 1.3 91.1 + - - +
274F VAL* 1.3 61.3 + - - +
275F HIS* 5.3 10.4 + - + +
320F VAL* 5.9 0.2 - - - -
321F GLN* 2.9 38.2 + - + +
322F SER* 3.7 15.4 + - - -
323F PHE* 4.1 1.4 + - - +
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Residues in contact with VAL 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F ARG* 3.1 2.7 - - - +
235F PHE* 2.8 36.7 + - + +
272F ARG* 4.2 8.3 - - - +
273F ASP* 1.3 77.4 - - - +
275F HIS* 1.3 68.8 + - - +
278F SER* 4.4 10.5 - - - -
279F LEU* 3.8 31.8 - - + +
312F LEU* 4.1 24.9 - - + +
313F PHE* 3.9 33.9 - - + -
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Residues in contact with HIS 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F SER 6.0 0.2 - - - -
233F GLY 3.7 11.2 - - - +
234F ARG* 3.9 25.3 + - + -
273F ASP* 5.3 9.3 + - + +
274F VAL* 1.3 79.6 - - - +
276F ASN* 1.3 66.9 + - - +
277F ARG* 3.8 38.0 + - + +
278F SER* 2.9 22.6 + - - +
279F LEU* 3.6 4.3 + - - +
321F GLN* 5.0 16.0 + - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il